Starting phenix.real_space_refine
on Fri May 16 09:19:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn6_40614/05_2025/8sn6_40614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn6_40614/05_2025/8sn6_40614.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/8sn6_40614/05_2025/8sn6_40614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn6_40614/05_2025/8sn6_40614.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn6_40614/05_2025/8sn6_40614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn6_40614/05_2025/8sn6_40614.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 17 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      32.578  74.262  46.883  1.00 88.39           S
  ATOM  12446  SG  CYS K  51      31.271  71.186  45.070  1.00 91.68           S
  ATOM  12470  SG  CYS K  54      32.612  74.141  43.059  1.00 96.59           S
  ATOM  12187  SG  CYS K  16      22.251  68.673  52.194  1.00104.88           S
  ATOM  12205  SG  CYS K  19      20.908  65.621  54.027  1.00100.49           S
  ATOM  12335  SG  CYS K  36      23.441  67.769  55.828  1.00 94.61           S
  ATOM  12357  SG  CYS K  39      24.460  65.513  53.151  1.00 91.60           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: 9.43, per 1000 atoms: 0.65
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (110.224, 134.128, 126.16, 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  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 3.38
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        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:
      46 helices and 13 sheets defined
      62.9% alpha, 5.9% beta
      135 base pairs and 253 stacking pairs defined.
    Time for finding SS restraints: 6.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 3.587A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.560A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (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: 3.873A  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: 3.846A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.504A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.564A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.672A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.539A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.824A  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: 3.600A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.029A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.529A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.696A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.697A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.775A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.806A  pdb=" N   CYS K  14 " --> pdb=" O   SER K  10 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 10 through 15'
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 3.749A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.502A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE K  80 " --> pdb=" O   LEU K  76 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN K  81 " --> pdb=" O   TRP K  77 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.859A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.686A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.926A  pdb=" N   VAL L 102 " --> pdb=" O   THR L  98 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU L 103 " --> pdb=" O   ILE L  99 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.921A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 145
      removed outlier: 3.918A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.612A  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 96 through 98
      removed outlier: 6.768A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 8.117A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.996A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.254A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.813A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28
      removed outlier: 3.805A  pdb=" N   VAL K  27 " --> pdb=" O   LEU K  35 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25
    Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16

    496 hydrogen bonds defined for protein.
    1461 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      253 stacking parallelities
  Total time for adding SS restraints: 5.00

  Time building geometry restraints manager: 4.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3591
        1.34 -     1.46: 4442
        1.46 -     1.58: 6804
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" CB  GLU K  25 "
       pdb=" CG  GLU K  25 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.90e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.454 -0.032 3.00e-02 1.11e+03 1.14e+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 9.68e-01
  bond pdb=" CB  MET D  59 "
       pdb=" CG  MET D  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.17e-01
  bond pdb=" C4'  DA I -35 "
       pdb=" C3'  DA I -35 "
    ideal  model  delta    sigma   weight residual
    1.523  1.504  0.019 2.00e-02 2.50e+03 8.82e-01
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 21517
        1.47 -     2.94: 587
        2.94 -     4.41: 37
        4.41 -     5.88: 23
        5.88 -     7.35: 7
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  127.56   -6.02 1.91e+00 2.74e-01 9.94e+00
  angle pdb=" CA  ARG L 125 "
        pdb=" CB  ARG L 125 "
        pdb=" CG  ARG L 125 "
      ideal   model   delta    sigma   weight residual
     114.10  120.06   -5.96 2.00e+00 2.50e-01 8.88e+00
  angle pdb=" C   ASN L 135 "
        pdb=" N   ARG L 136 "
        pdb=" CA  ARG L 136 "
      ideal   model   delta    sigma   weight residual
     121.14  116.17    4.97 1.75e+00 3.27e-01 8.08e+00
  angle pdb=" CB  GLU K  25 "
        pdb=" CG  GLU K  25 "
        pdb=" CD  GLU K  25 "
      ideal   model   delta    sigma   weight residual
     112.60  117.37   -4.77 1.70e+00 3.46e-01 7.86e+00
  angle pdb=" C   PHE L  62 "
        pdb=" N   LYS L  63 "
        pdb=" CA  LYS L  63 "
      ideal   model   delta    sigma   weight residual
     122.74  129.55   -6.81 2.44e+00 1.68e-01 7.78e+00
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.23: 7238
       35.23 -    70.47: 1347
       70.47 -   105.70: 24
      105.70 -   140.94: 0
      140.94 -   176.17: 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
    -140.00   36.17 -176.17     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   71.38  148.62     1      3.50e+01 8.16e-04 1.45e+01
  dihedral pdb=" CB  GLU G  56 "
           pdb=" CG  GLU G  56 "
           pdb=" CD  GLU G  56 "
           pdb=" OE1 GLU G  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.89   88.89     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1770
       0.032 -    0.064: 575
       0.064 -    0.096: 112
       0.096 -    0.128: 53
       0.128 -    0.160: 6
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  ARG L 125 "
            pdb=" N   ARG L 125 "
            pdb=" C   ARG L 125 "
            pdb=" CB  ARG L 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.38e-01
  chirality pdb=" CA  LYS L 101 "
            pdb=" N   LYS L 101 "
            pdb=" C   LYS L 101 "
            pdb=" CB  LYS L 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU K  25 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   GLU K  25 "    0.038 2.00e-02 2.50e+03
        pdb=" O   GLU K  25 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PRO K  26 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.024 2.00e-02 2.50e+03   1.02e-02 2.84e+00
        pdb=" N9   DA I -35 "    0.021 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.000 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  33 "    0.009 2.00e-02 2.50e+03   1.02e-02 2.60e+00
        pdb=" CG  TRP L  33 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  33 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  33 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  33 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  33 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  33 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  33 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  33 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  33 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 233
        2.65 -     3.21: 12387
        3.21 -     3.77: 25809
        3.77 -     4.34: 32710
        4.34 -     4.90: 48516
  Nonbonded interactions: 119655
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.084 2.496
  nonbonded pdb=" O   ARG L 125 "
            pdb=" OG1 THR L 129 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   ASN G  73 "
            pdb=" ND2 ASN G  73 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.228 3.040
  ... (remaining 119650 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.17 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:             0.850
  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:          0.630
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     41.640
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
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   0.041  15482  Z= 0.169
  Angle     :  0.572   7.352  22186  Z= 0.327
  Chirality :  0.035   0.160   2516
  Planarity :  0.004   0.038   1794
  Dihedral  : 25.930 176.171   6577
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.22 %
    Favored  : 99.68 %
  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:  1.99 (0.26), residues: 1057
  helix:  2.41 (0.21), residues: 626
  sheet:  1.10 (0.75), residues: 50
  loop : -0.53 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP L  33 
 HIS   0.002   0.001   HIS K  65 
 PHE   0.015   0.001   PHE L  56 
 TYR   0.018   0.001   TYR H  83 
 ARG   0.006   0.000   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00129 (    2)
  link_TRANS           : angle       0.51959 (    6)
  hydrogen bonds       : bond        0.10679 (  843)
  hydrogen bonds       : angle       4.14569 ( 2151)
  metal coordination   : bond        0.01060 (    8)
  metal coordination   : angle       4.15496 (    9)
  covalent geometry    : bond        0.00378 (15472)
  covalent geometry    : angle       0.56589 (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
  243 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.176 
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: A   81 ASP cc_start: 0.8084 (m-30) cc_final: 0.7869 (m-30)
REVERT: A   94 GLU cc_start: 0.8400 (tp30) cc_final: 0.7955 (mm-30)
REVERT: C   75 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8550 (mttm)
REVERT: C   95 LYS cc_start: 0.8850 (tptt) cc_final: 0.8643 (tptm)
REVERT: D   33 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7873 (mtp-110)
REVERT: D   86 ARG cc_start: 0.8743 (mmt-90) cc_final: 0.8382 (mmt90)
REVERT: H  100 LEU cc_start: 0.9442 (mt) cc_final: 0.9172 (mp)
REVERT: K   42 SER cc_start: 0.7939 (p) cc_final: 0.7269 (p)
REVERT: K   66 THR cc_start: 0.7827 (m) cc_final: 0.7608 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.3256
  time to fit residues: 106.6892
Evaluate side-chains
  199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
D  95 GLN
G  73 ASN
L  20 GLN
L  32 HIS
M  41 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.129765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.088554 restraints weight = 33855.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.087831 restraints weight = 29856.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.088481 restraints weight = 30114.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  15482  Z= 0.193
  Angle     :  0.616  15.138  22186  Z= 0.342
  Chirality :  0.036   0.257   2516
  Planarity :  0.004   0.039   1794
  Dihedral  : 28.864 176.060   4413
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.74 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.26), residues: 1057
  helix:  2.33 (0.21), residues: 648
  sheet:  0.99 (0.70), residues: 55
  loop : -0.63 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP L  33 
 HIS   0.005   0.001   HIS K  33 
 PHE   0.035   0.002   PHE L  62 
 TYR   0.030   0.002   TYR H  83 
 ARG   0.006   0.000   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00205 (    2)
  link_TRANS           : angle       0.46255 (    6)
  hydrogen bonds       : bond        0.04952 (  843)
  hydrogen bonds       : angle       3.51606 ( 2151)
  metal coordination   : bond        0.03087 (    8)
  metal coordination   : angle       6.72258 (    9)
  covalent geometry    : bond        0.00438 (15472)
  covalent geometry    : angle       0.60146 (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
  220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 208
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8100 (m-30) cc_final: 0.7889 (m-30)
REVERT: A   94 GLU cc_start: 0.8363 (tp30) cc_final: 0.8079 (mm-30)
REVERT: C   95 LYS cc_start: 0.8939 (tptt) cc_final: 0.8676 (tptm)
REVERT: D   33 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7812 (mtp-110)
REVERT: D   86 ARG cc_start: 0.8778 (mmt-90) cc_final: 0.8356 (mmt90)
REVERT: E  125 GLN cc_start: 0.8428 (mt0) cc_final: 0.8185 (mp10)
REVERT: H  100 LEU cc_start: 0.9432 (mt) cc_final: 0.9161 (mp)
REVERT: K   66 THR cc_start: 0.8211 (m) cc_final: 0.7911 (m)
REVERT: K   68 ARG cc_start: 0.7284 (ptp90) cc_final: 0.6721 (mtm180)
REVERT: L    8 LYS cc_start: 0.8468 (mppt) cc_final: 0.8214 (tptp)
  outliers start: 12
  outliers final: 9
  residues processed: 215
  average time/residue: 0.3283
  time to fit residues: 96.1367
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 192
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
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   91 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain H residue   35 GLU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 128 optimal weight:   40.0000
   chunk 50 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 126 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 104 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.129701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.079487 restraints weight = 54330.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.080877 restraints weight = 30407.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.081392 restraints weight = 21394.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  15482  Z= 0.168
  Angle     :  0.587  10.274  22186  Z= 0.329
  Chirality :  0.035   0.173   2516
  Planarity :  0.004   0.042   1794
  Dihedral  : 28.737 176.425   4413
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.88 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.26), residues: 1057
  helix:  2.40 (0.21), residues: 649
  sheet:  1.15 (0.73), residues: 50
  loop : -0.71 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L  33 
 HIS   0.005   0.001   HIS L   0 
 PHE   0.034   0.002   PHE L  62 
 TYR   0.035   0.002   TYR L 134 
 ARG   0.006   0.000   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00099 (    2)
  link_TRANS           : angle       0.38828 (    6)
  hydrogen bonds       : bond        0.04562 (  843)
  hydrogen bonds       : angle       3.31815 ( 2151)
  metal coordination   : bond        0.02229 (    8)
  metal coordination   : angle       5.40376 (    9)
  covalent geometry    : bond        0.00375 (15472)
  covalent geometry    : angle       0.57677 (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
  220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8232 (m-30) cc_final: 0.8023 (m-30)
REVERT: A   94 GLU cc_start: 0.8343 (tp30) cc_final: 0.8096 (mm-30)
REVERT: C   95 LYS cc_start: 0.8904 (tptt) cc_final: 0.8654 (tptm)
REVERT: D   33 ARG cc_start: 0.8230 (mtp-110) cc_final: 0.7716 (mtp-110)
REVERT: D   86 ARG cc_start: 0.8748 (mmt-90) cc_final: 0.8343 (mmt90)
REVERT: E   94 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7672 (mm-30)
REVERT: E  125 GLN cc_start: 0.8410 (mt0) cc_final: 0.8122 (mp10)
REVERT: K   66 THR cc_start: 0.8218 (m) cc_final: 0.7940 (m)
REVERT: K   68 ARG cc_start: 0.7565 (ptp90) cc_final: 0.6936 (mtm180)
REVERT: L    8 LYS cc_start: 0.8896 (mppt) cc_final: 0.8412 (tptp)
REVERT: L   74 TYR cc_start: 0.8495 (t80) cc_final: 0.7964 (t80)
REVERT: L   75 HIS cc_start: 0.8819 (t-90) cc_final: 0.8476 (t-90)
REVERT: L   97 LEU cc_start: 0.8377 (tp) cc_final: 0.8173 (tt)
REVERT: L  134 TYR cc_start: 0.7568 (t80) cc_final: 0.7163 (t80)
REVERT: M   42 ARG cc_start: 0.7399 (mmt180) cc_final: 0.7062 (mmt180)
  outliers start: 18
  outliers final: 12
  residues processed: 210
  average time/residue: 0.3284
  time to fit residues: 94.2172
Evaluate side-chains
  203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 191
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
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   56 GLU
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain K residue   37 LYS
Chi-restraints excluded: chain L residue   45 TYR
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 105 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 72 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  49 HIS
L  32 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.128414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.077289 restraints weight = 48236.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.078309 restraints weight = 26915.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.078982 restraints weight = 21322.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  15482  Z= 0.182
  Angle     :  0.593  10.516  22186  Z= 0.331
  Chirality :  0.036   0.308   2516
  Planarity :  0.004   0.043   1794
  Dihedral  : 28.752 176.091   4413
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.96 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.94 (0.26), residues: 1057
  helix:  2.35 (0.20), residues: 649
  sheet:  1.26 (0.74), residues: 50
  loop : -0.76 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP L  93 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.034   0.002   PHE L  62 
 TYR   0.022   0.002   TYR H  83 
 ARG   0.007   0.000   ARG K  55 

Details of bonding type rmsd
  link_TRANS           : bond        0.00055 (    2)
  link_TRANS           : angle       0.41634 (    6)
  hydrogen bonds       : bond        0.04715 (  843)
  hydrogen bonds       : angle       3.29746 ( 2151)
  metal coordination   : bond        0.02015 (    8)
  metal coordination   : angle       5.71310 (    9)
  covalent geometry    : bond        0.00412 (15472)
  covalent geometry    : angle       0.58227 (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
  215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 195
  time to evaluate  : 1.218 
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: A   94 GLU cc_start: 0.8333 (tp30) cc_final: 0.8044 (mm-30)
REVERT: C   73 ASN cc_start: 0.8234 (t0) cc_final: 0.8025 (t0)
REVERT: C   95 LYS cc_start: 0.9041 (tptt) cc_final: 0.8691 (tptm)
REVERT: D   33 ARG cc_start: 0.8180 (mtp-110) cc_final: 0.7677 (mtp-110)
REVERT: D   86 ARG cc_start: 0.8877 (mmt-90) cc_final: 0.8399 (mmt90)
REVERT: E   94 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7724 (mm-30)
REVERT: E  125 GLN cc_start: 0.8479 (mt0) cc_final: 0.8230 (mt0)
REVERT: K   66 THR cc_start: 0.8190 (m) cc_final: 0.7942 (m)
REVERT: K   68 ARG cc_start: 0.7544 (ptp90) cc_final: 0.7133 (mtm180)
REVERT: L    4 LYS cc_start: 0.9255 (mptt) cc_final: 0.9014 (mptt)
REVERT: L    8 LYS cc_start: 0.8959 (mppt) cc_final: 0.8447 (tptp)
REVERT: L   74 TYR cc_start: 0.8578 (t80) cc_final: 0.7751 (t80)
REVERT: L   75 HIS cc_start: 0.8848 (t-90) cc_final: 0.8592 (t-90)
REVERT: L  134 TYR cc_start: 0.8000 (t80) cc_final: 0.7151 (t80)
REVERT: L  145 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.6054 (m-10)
  outliers start: 20
  outliers final: 13
  residues processed: 205
  average time/residue: 0.3428
  time to fit residues: 95.5491
Evaluate side-chains
  203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 189
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
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   19 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  143 GLN
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 125 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0570
   chunk 2 optimal weight:    0.0270
   chunk 112 optimal weight:    0.1980
   chunk 45 optimal weight:    0.0470
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.2454

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.131318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.093211 restraints weight = 45404.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.092672 restraints weight = 48358.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.093629 restraints weight = 38716.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15482  Z= 0.137
  Angle     :  0.574  12.138  22186  Z= 0.319
  Chirality :  0.034   0.293   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 28.608 177.495   4413
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.39 %
    Favored  : 84.09 %
  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:  2.19 (0.26), residues: 1057
  helix:  2.52 (0.21), residues: 649
  sheet:  1.46 (0.74), residues: 50
  loop : -0.61 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP L  93 
 HIS   0.003   0.000   HIS B  75 
 PHE   0.011   0.001   PHE L  62 
 TYR   0.014   0.001   TYR L  74 
 ARG   0.009   0.000   ARG L 136 

Details of bonding type rmsd
  link_TRANS           : bond        0.00129 (    2)
  link_TRANS           : angle       0.22134 (    6)
  hydrogen bonds       : bond        0.03903 (  843)
  hydrogen bonds       : angle       3.03713 ( 2151)
  metal coordination   : bond        0.01609 (    8)
  metal coordination   : angle       5.60113 (    9)
  covalent geometry    : bond        0.00286 (15472)
  covalent geometry    : angle       0.56332 (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
  226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 212
  time to evaluate  : 1.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.7999 (tp30) cc_final: 0.7698 (mm-30)
REVERT: C   73 ASN cc_start: 0.8340 (t0) cc_final: 0.8105 (t0)
REVERT: C   95 LYS cc_start: 0.8879 (tptt) cc_final: 0.8595 (tptm)
REVERT: D   33 ARG cc_start: 0.8271 (mtp-110) cc_final: 0.7793 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8787 (pm20) cc_final: 0.8397 (pm20)
REVERT: E  125 GLN cc_start: 0.8381 (mt0) cc_final: 0.8081 (mt0)
REVERT: H  119 THR cc_start: 0.9477 (t) cc_final: 0.9266 (t)
REVERT: K   66 THR cc_start: 0.8287 (m) cc_final: 0.7942 (m)
REVERT: L    8 LYS cc_start: 0.8614 (mppt) cc_final: 0.8268 (tptp)
REVERT: L   69 PHE cc_start: 0.7467 (m-80) cc_final: 0.7155 (m-80)
REVERT: L   97 LEU cc_start: 0.8343 (tt) cc_final: 0.8125 (tp)
REVERT: L  145 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5608 (m-10)
  outliers start: 14
  outliers final: 7
  residues processed: 219
  average time/residue: 0.3301
  time to fit residues: 97.8910
Evaluate side-chains
  208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 200
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 120 optimal weight:    6.9990
   chunk 124 optimal weight:    8.9990
   chunk 85 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
L  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.126406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.076447 restraints weight = 46710.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.076397 restraints weight = 27838.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.076620 restraints weight = 21403.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2816
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2815
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  15482  Z= 0.271
  Angle     :  0.659  12.232  22186  Z= 0.363
  Chirality :  0.039   0.298   2516
  Planarity :  0.005   0.062   1794
  Dihedral  : 28.861 175.059   4413
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.58 %
    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:  1.78 (0.26), residues: 1057
  helix:  2.19 (0.20), residues: 648
  sheet:  1.19 (0.73), residues: 50
  loop : -0.73 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L  93 
 HIS   0.006   0.001   HIS L  75 
 PHE   0.015   0.002   PHE L  62 
 TYR   0.031   0.002   TYR L 134 
 ARG   0.008   0.001   ARG K  55 

Details of bonding type rmsd
  link_TRANS           : bond        0.00173 (    2)
  link_TRANS           : angle       0.49401 (    6)
  hydrogen bonds       : bond        0.05452 (  843)
  hydrogen bonds       : angle       3.49936 ( 2151)
  metal coordination   : bond        0.02178 (    8)
  metal coordination   : angle       5.91278 (    9)
  covalent geometry    : bond        0.00641 (15472)
  covalent geometry    : angle       0.64808 (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
  220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8391 (tp30) cc_final: 0.8076 (mm-30)
REVERT: C   16 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8135 (t)
REVERT: C   73 ASN cc_start: 0.8274 (t0) cc_final: 0.8055 (t0)
REVERT: C   95 LYS cc_start: 0.9079 (tptt) cc_final: 0.8705 (tptm)
REVERT: D   33 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7696 (mtp-110)
REVERT: E  125 GLN cc_start: 0.8544 (mt0) cc_final: 0.8262 (mt0)
REVERT: H   46 LYS cc_start: 0.9178 (tppt) cc_final: 0.8792 (mmtm)
REVERT: H   59 MET cc_start: 0.8706 (tpp) cc_final: 0.8460 (tpt)
REVERT: K   66 THR cc_start: 0.8256 (m) cc_final: 0.8027 (m)
REVERT: L    8 LYS cc_start: 0.8958 (mppt) cc_final: 0.8537 (tptp)
REVERT: L   74 TYR cc_start: 0.8616 (t80) cc_final: 0.8187 (t80)
REVERT: L   75 HIS cc_start: 0.8854 (t-90) cc_final: 0.8562 (t-90)
REVERT: L  134 TYR cc_start: 0.7687 (t80) cc_final: 0.7110 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 209
  average time/residue: 0.3235
  time to fit residues: 92.0140
Evaluate side-chains
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 192
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 123 optimal weight:    6.9990
   chunk 52 optimal weight:    0.6980
   chunk 128 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 118 optimal weight:    0.8980
   chunk 111 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.128505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.077123 restraints weight = 49905.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.078688 restraints weight = 27527.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.079240 restraints weight = 20231.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15482  Z= 0.164
  Angle     :  0.606  13.210  22186  Z= 0.335
  Chirality :  0.036   0.323   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 28.785 176.379   4413
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.99 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.26), residues: 1057
  helix:  2.30 (0.21), residues: 649
  sheet:  1.18 (0.73), residues: 50
  loop : -0.70 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L  93 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.013   0.001   PHE L  62 
 TYR   0.018   0.001   TYR H  83 
 ARG   0.010   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00081 (    2)
  link_TRANS           : angle       0.34967 (    6)
  hydrogen bonds       : bond        0.04554 (  843)
  hydrogen bonds       : angle       3.24990 ( 2151)
  metal coordination   : bond        0.01800 (    8)
  metal coordination   : angle       5.96686 (    9)
  covalent geometry    : bond        0.00366 (15472)
  covalent geometry    : angle       0.59452 (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
  215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   16 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8180 (t)
REVERT: C   19 SER cc_start: 0.9415 (OUTLIER) cc_final: 0.9200 (t)
REVERT: C   73 ASN cc_start: 0.8309 (t0) cc_final: 0.8072 (t0)
REVERT: C   95 LYS cc_start: 0.9008 (tptt) cc_final: 0.8675 (tptm)
REVERT: D   33 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7743 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8824 (pm20) cc_final: 0.8509 (pm20)
REVERT: E  125 GLN cc_start: 0.8527 (mt0) cc_final: 0.8216 (mt0)
REVERT: H   46 LYS cc_start: 0.9150 (tppt) cc_final: 0.8726 (mmtm)
REVERT: H  119 THR cc_start: 0.9553 (t) cc_final: 0.9273 (t)
REVERT: K   66 THR cc_start: 0.8201 (m) cc_final: 0.7932 (m)
REVERT: L    8 LYS cc_start: 0.8985 (mppt) cc_final: 0.8513 (tptp)
REVERT: L   69 PHE cc_start: 0.8159 (m-80) cc_final: 0.7916 (m-80)
REVERT: L   74 TYR cc_start: 0.8599 (t80) cc_final: 0.7901 (t80)
REVERT: L   75 HIS cc_start: 0.8837 (t-90) cc_final: 0.8548 (t-90)
REVERT: L   93 TRP cc_start: 0.8582 (t-100) cc_final: 0.8350 (t-100)
REVERT: L  134 TYR cc_start: 0.7979 (t80) cc_final: 0.7177 (t80)
  outliers start: 17
  outliers final: 12
  residues processed: 206
  average time/residue: 0.3374
  time to fit residues: 94.3345
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 195
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
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   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
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:    0.5980
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 123 optimal weight:   20.0000
   chunk 42 optimal weight:    0.5980
   chunk 126 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 115 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** 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 = 0.3692 r_free = 0.3692 target = 0.128849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.077487 restraints weight = 48818.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.078971 restraints weight = 27749.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.079571 restraints weight = 21621.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1750

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= 0.160
  Angle     :  0.614  13.729  22186  Z= 0.336
  Chirality :  0.036   0.336   2516
  Planarity :  0.004   0.047   1794
  Dihedral  : 28.757 176.531   4413
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.97 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.26), residues: 1057
  helix:  2.33 (0.21), residues: 650
  sheet:  1.18 (0.73), residues: 50
  loop : -0.67 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L  93 
 HIS   0.004   0.001   HIS L   0 
 PHE   0.012   0.001   PHE L  62 
 TYR   0.018   0.001   TYR H  83 
 ARG   0.013   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00073 (    2)
  link_TRANS           : angle       0.30897 (    6)
  hydrogen bonds       : bond        0.04388 (  843)
  hydrogen bonds       : angle       3.19893 ( 2151)
  metal coordination   : bond        0.01700 (    8)
  metal coordination   : angle       5.33228 (    9)
  covalent geometry    : bond        0.00355 (15472)
  covalent geometry    : angle       0.60522 (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
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 197
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8359 (tp30) cc_final: 0.8105 (mm-30)
REVERT: C   16 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8047 (t)
REVERT: C   19 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9183 (t)
REVERT: C   73 ASN cc_start: 0.8325 (t0) cc_final: 0.8103 (t0)
REVERT: C   95 LYS cc_start: 0.8989 (tptt) cc_final: 0.8649 (tptm)
REVERT: D   33 ARG cc_start: 0.8256 (mtp-110) cc_final: 0.7737 (mtp-110)
REVERT: E   94 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7936 (mm-30)
REVERT: E  125 GLN cc_start: 0.8530 (mt0) cc_final: 0.8218 (mt0)
REVERT: H   46 LYS cc_start: 0.9143 (tppt) cc_final: 0.8768 (tppt)
REVERT: H  119 THR cc_start: 0.9560 (t) cc_final: 0.9279 (t)
REVERT: K   66 THR cc_start: 0.8319 (m) cc_final: 0.8004 (m)
REVERT: L    8 LYS cc_start: 0.9032 (mppt) cc_final: 0.8568 (tptp)
REVERT: L    9 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8347 (mm-30)
REVERT: L   60 TYR cc_start: 0.8679 (t80) cc_final: 0.8357 (t80)
REVERT: L   69 PHE cc_start: 0.8191 (m-80) cc_final: 0.7920 (m-80)
REVERT: L   74 TYR cc_start: 0.8743 (t80) cc_final: 0.7858 (t80)
REVERT: L   75 HIS cc_start: 0.8795 (t-90) cc_final: 0.8545 (t-90)
REVERT: L  134 TYR cc_start: 0.8061 (t80) cc_final: 0.7171 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 206
  average time/residue: 0.3368
  time to fit residues: 93.7187
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 195
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
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   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
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:    0.2980
   chunk 73 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 49 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** 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 = 0.3663 r_free = 0.3663 target = 0.126648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.085931 restraints weight = 37371.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.084756 restraints weight = 35361.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.085965 restraints weight = 29154.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2977
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2977
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  15482  Z= 0.225
  Angle     :  0.660  13.801  22186  Z= 0.358
  Chirality :  0.038   0.326   2516
  Planarity :  0.004   0.046   1794
  Dihedral  : 28.890 175.546   4413
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  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:  1.71 (0.26), residues: 1057
  helix:  2.12 (0.20), residues: 648
  sheet:  1.15 (0.73), residues: 50
  loop : -0.74 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP L  93 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.012   0.002   PHE L  62 
 TYR   0.022   0.002   TYR H  83 
 ARG   0.016   0.001   ARG L 136 

Details of bonding type rmsd
  link_TRANS           : bond        0.00144 (    2)
  link_TRANS           : angle       0.44914 (    6)
  hydrogen bonds       : bond        0.05141 (  843)
  hydrogen bonds       : angle       3.41423 ( 2151)
  metal coordination   : bond        0.02011 (    8)
  metal coordination   : angle       5.64542 (    9)
  covalent geometry    : bond        0.00524 (15472)
  covalent geometry    : angle       0.64988 (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
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8401 (tp30) cc_final: 0.8086 (mm-30)
REVERT: C   73 ASN cc_start: 0.8441 (t0) cc_final: 0.8226 (t0)
REVERT: C   95 LYS cc_start: 0.9078 (tptt) cc_final: 0.8700 (tptm)
REVERT: D   33 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7700 (mtp-110)
REVERT: E  125 GLN cc_start: 0.8521 (mt0) cc_final: 0.8206 (mt0)
REVERT: H   46 LYS cc_start: 0.9203 (tppt) cc_final: 0.8860 (tppt)
REVERT: H  119 THR cc_start: 0.9557 (t) cc_final: 0.9289 (t)
REVERT: K   66 THR cc_start: 0.8363 (m) cc_final: 0.8099 (m)
REVERT: L    9 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7675 (mm-30)
REVERT: L   69 PHE cc_start: 0.7678 (m-80) cc_final: 0.7451 (m-80)
REVERT: L   75 HIS cc_start: 0.8495 (t-90) cc_final: 0.8077 (t-90)
  outliers start: 17
  outliers final: 14
  residues processed: 206
  average time/residue: 0.3369
  time to fit residues: 94.1342
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 195
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 45 optimal weight:    0.0670
   chunk 101 optimal weight:    8.9990
   chunk 115 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0000
   chunk 76 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.5322

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** 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 = 0.3701 r_free = 0.3701 target = 0.129463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.089015 restraints weight = 36966.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.087223 restraints weight = 32300.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.087869 restraints weight = 40064.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15482  Z= 0.152
  Angle     :  0.640  14.935  22186  Z= 0.349
  Chirality :  0.036   0.316   2516
  Planarity :  0.004   0.052   1794
  Dihedral  : 28.763 177.189   4413
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.72 %
    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:  1.95 (0.26), residues: 1057
  helix:  2.33 (0.21), residues: 649
  sheet:  1.30 (0.75), residues: 49
  loop : -0.68 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L  93 
 HIS   0.003   0.000   HIS B  75 
 PHE   0.013   0.001   PHE L  62 
 TYR   0.047   0.002   TYR L 134 
 ARG   0.014   0.001   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00083 (    2)
  link_TRANS           : angle       0.26443 (    6)
  hydrogen bonds       : bond        0.04244 (  843)
  hydrogen bonds       : angle       3.18829 ( 2151)
  metal coordination   : bond        0.01563 (    8)
  metal coordination   : angle       4.89076 (    9)
  covalent geometry    : bond        0.00330 (15472)
  covalent geometry    : angle       0.63306 (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
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 199
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8320 (tp30) cc_final: 0.8014 (mm-30)
REVERT: C   95 LYS cc_start: 0.9013 (tptt) cc_final: 0.8676 (tptm)
REVERT: D   33 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7715 (mtp-110)
REVERT: E  125 GLN cc_start: 0.8464 (mt0) cc_final: 0.8121 (mt0)
REVERT: H   46 LYS cc_start: 0.9164 (tppt) cc_final: 0.8800 (tppt)
REVERT: H  119 THR cc_start: 0.9510 (t) cc_final: 0.9247 (t)
REVERT: K   66 THR cc_start: 0.8357 (m) cc_final: 0.8032 (m)
REVERT: L   69 PHE cc_start: 0.7694 (m-80) cc_final: 0.7477 (m-80)
REVERT: L   75 HIS cc_start: 0.8376 (t-90) cc_final: 0.8028 (t-90)
  outliers start: 14
  outliers final: 13
  residues processed: 208
  average time/residue: 0.3329
  time to fit residues: 94.0192
Evaluate side-chains
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 193
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 110 optimal weight:    7.9990
   chunk 111 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 115 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.126092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.074276 restraints weight = 58069.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.075868 restraints weight = 29796.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.077841 restraints weight = 20589.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  15482  Z= 0.243
  Angle     :  0.699  14.042  22186  Z= 0.378
  Chirality :  0.039   0.314   2516
  Planarity :  0.005   0.044   1794
  Dihedral  : 28.920 175.480   4413
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.40 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.26), residues: 1057
  helix:  2.07 (0.21), residues: 648
  sheet:  1.24 (0.75), residues: 50
  loop : -0.78 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP L  33 
 HIS   0.005   0.001   HIS L   0 
 PHE   0.017   0.002   PHE L  62 
 TYR   0.044   0.002   TYR L 134 
 ARG   0.013   0.001   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00180 (    2)
  link_TRANS           : angle       0.47338 (    6)
  hydrogen bonds       : bond        0.05281 (  843)
  hydrogen bonds       : angle       3.50837 ( 2151)
  metal coordination   : bond        0.01834 (    8)
  metal coordination   : angle       6.25883 (    9)
  covalent geometry    : bond        0.00567 (15472)
  covalent geometry    : angle       0.68725 (22171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4703.23 seconds
wall clock time: 82 minutes 34.66 seconds (4954.66 seconds total)