Starting phenix.real_space_refine
on Thu Jun 12 20:04:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn6_40614/06_2025/8sn6_40614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn6_40614/06_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_40614/06_2025/8sn6_40614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn6_40614/06_2025/8sn6_40614.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn6_40614/06_2025/8sn6_40614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn6_40614/06_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.77, per 1000 atoms: 0.60
  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: 3.14
  Conformation dependent library (CDL) restraints added in 1.3 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: 6.07
  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: 5.05

  Time building geometry restraints manager: 3.82 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:             0.990
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     39.640
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.410
-------------------------------------------------------------------------------
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  : 1.152 
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: 0.3375
  time to fit residues: 110.9044
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  : 1.153 
-------------------------------------------------------------------------------
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 = 29856.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.088481 restraints weight = 30114.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
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: 0.8451
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  : 1.200 
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: 0.8104 (m-30) cc_final: 0.7892 (m-30)
REVERT: A   94 GLU cc_start: 0.8364 (tp30) cc_final: 0.8080 (mm-30)
REVERT: C   95 LYS cc_start: 0.8940 (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: 0.8780 (mmt-90) cc_final: 0.8357 (mmt90)
REVERT: E  125 GLN cc_start: 0.8431 (mt0) cc_final: 0.8186 (mp10)
REVERT: H  100 LEU cc_start: 0.9431 (mt) cc_final: 0.9160 (mp)
REVERT: K   66 THR cc_start: 0.8211 (m) cc_final: 0.7912 (m)
REVERT: K   68 ARG cc_start: 0.7287 (ptp90) cc_final: 0.6722 (mtm180)
REVERT: L    8 LYS cc_start: 0.8471 (mppt) cc_final: 0.8215 (tptp)
  outliers start: 12
  outliers final: 9
  residues processed: 215
  average time/residue: 0.3227
  time to fit residues: 94.9346
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  : 1.094 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 126 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.129603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.078867 restraints weight = 54419.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.080909 restraints weight = 26528.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.080716 restraints weight = 16458.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    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 = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  15482  Z= 0.171
  Angle     :  0.586  10.110  22186  Z= 0.329
  Chirality :  0.035   0.179   2516
  Planarity :  0.004   0.042   1794
  Dihedral  : 28.735 176.396   4413
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.77 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.20), residues: 649
  sheet:  1.16 (0.73), residues: 50
  loop : -0.71 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP L  33 
 HIS   0.006   0.001   HIS L   0 
 PHE   0.030   0.002   PHE L  62 
 TYR   0.030   0.002   TYR L 134 
 ARG   0.007   0.000   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00094 (    2)
  link_TRANS           : angle       0.39043 (    6)
  hydrogen bonds       : bond        0.04593 (  843)
  hydrogen bonds       : angle       3.31666 ( 2151)
  metal coordination   : bond        0.02281 (    8)
  metal coordination   : angle       5.41009 (    9)
  covalent geometry    : bond        0.00383 (15472)
  covalent geometry    : angle       0.57615 (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
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 203
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8365 (m-30) cc_final: 0.8154 (m-30)
REVERT: A   94 GLU cc_start: 0.8338 (tp30) cc_final: 0.8077 (mm-30)
REVERT: C   95 LYS cc_start: 0.8968 (tptt) cc_final: 0.8676 (tptm)
REVERT: D   33 ARG cc_start: 0.8218 (mtp-110) cc_final: 0.7699 (mtp-110)
REVERT: D   86 ARG cc_start: 0.8853 (mmt-90) cc_final: 0.8398 (mmt90)
REVERT: E  125 GLN cc_start: 0.8482 (mt0) cc_final: 0.8160 (mp10)
REVERT: K   66 THR cc_start: 0.8168 (m) cc_final: 0.7902 (m)
REVERT: K   68 ARG cc_start: 0.7689 (ptp90) cc_final: 0.6985 (mtm180)
REVERT: L    8 LYS cc_start: 0.8939 (mppt) cc_final: 0.8457 (tptp)
REVERT: L   74 TYR cc_start: 0.8506 (t80) cc_final: 0.7931 (t80)
REVERT: L   75 HIS cc_start: 0.8827 (t-90) cc_final: 0.8468 (t-90)
REVERT: L   97 LEU cc_start: 0.8376 (tp) cc_final: 0.8150 (tt)
REVERT: L  134 TYR cc_start: 0.7662 (t80) cc_final: 0.7210 (t80)
REVERT: M   42 ARG cc_start: 0.7452 (mmt180) cc_final: 0.7131 (mmt180)
  outliers start: 18
  outliers final: 12
  residues processed: 211
  average time/residue: 0.3265
  time to fit residues: 94.1293
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 192
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   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:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
H  49 HIS
L  32 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.127257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.073895 restraints weight = 48424.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.075974 restraints weight = 26241.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.077370 restraints weight = 18419.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  15482  Z= 0.206
  Angle     :  0.608  10.449  22186  Z= 0.339
  Chirality :  0.037   0.286   2516
  Planarity :  0.004   0.042   1794
  Dihedral  : 28.802 175.696   4413
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.07 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.26), residues: 1057
  helix:  2.28 (0.20), residues: 649
  sheet:  1.22 (0.73), residues: 50
  loop : -0.79 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP L  93 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.032   0.002   PHE L  62 
 TYR   0.023   0.002   TYR H  83 
 ARG   0.008   0.001   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00071 (    2)
  link_TRANS           : angle       0.48635 (    6)
  hydrogen bonds       : bond        0.05010 (  843)
  hydrogen bonds       : angle       3.37266 ( 2151)
  metal coordination   : bond        0.02185 (    8)
  metal coordination   : angle       5.85447 (    9)
  covalent geometry    : bond        0.00474 (15472)
  covalent geometry    : angle       0.59704 (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
  218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 1.085 
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   94 GLU cc_start: 0.8393 (tp30) cc_final: 0.8085 (mm-30)
REVERT: C   95 LYS cc_start: 0.9062 (tptt) cc_final: 0.8717 (tptm)
REVERT: D   33 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7671 (mtp-110)
REVERT: D   86 ARG cc_start: 0.8883 (mmt-90) cc_final: 0.8426 (mmt90)
REVERT: E   59 GLU cc_start: 0.8779 (pm20) cc_final: 0.8409 (pm20)
REVERT: E  125 GLN cc_start: 0.8503 (mt0) cc_final: 0.8246 (mt0)
REVERT: K   66 THR cc_start: 0.8244 (m) cc_final: 0.7995 (m)
REVERT: K   68 ARG cc_start: 0.7379 (ptp90) cc_final: 0.7071 (mtm180)
REVERT: L    4 LYS cc_start: 0.9221 (mptt) cc_final: 0.9002 (mptt)
REVERT: L    8 LYS cc_start: 0.8935 (mppt) cc_final: 0.8439 (tptp)
REVERT: L   74 TYR cc_start: 0.8647 (t80) cc_final: 0.7769 (t80)
REVERT: L   75 HIS cc_start: 0.8902 (t-90) cc_final: 0.8648 (t-90)
REVERT: L  134 TYR cc_start: 0.8013 (t80) cc_final: 0.7141 (t80)
  outliers start: 25
  outliers final: 17
  residues processed: 205
  average time/residue: 0.3366
  time to fit residues: 93.8853
Evaluate side-chains
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 189
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
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 H residue  118 VAL
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   50 PHE
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:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0370
   chunk 2 optimal weight:    0.8980
   chunk 112 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0270
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.5116

-------------------------------------------------------------------------------
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**
** F  93 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 = 0.3705 r_free = 0.3705 target = 0.129608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.090206 restraints weight = 45258.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.090615 restraints weight = 39406.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.090942 restraints weight = 38755.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15482  Z= 0.144
  Angle     :  0.580  12.218  22186  Z= 0.322
  Chirality :  0.035   0.296   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 28.683 177.118   4413
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.04 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.26), residues: 1057
  helix:  2.47 (0.21), residues: 649
  sheet:  1.42 (0.74), residues: 50
  loop : -0.66 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L  93 
 HIS   0.003   0.000   HIS B  75 
 PHE   0.032   0.001   PHE L  62 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.009   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00112 (    2)
  link_TRANS           : angle       0.27877 (    6)
  hydrogen bonds       : bond        0.04182 (  843)
  hydrogen bonds       : angle       3.11425 ( 2151)
  metal coordination   : bond        0.01661 (    8)
  metal coordination   : angle       5.89755 (    9)
  covalent geometry    : bond        0.00311 (15472)
  covalent geometry    : angle       0.56786 (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
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 205
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8126 (tp30) cc_final: 0.7764 (mm-30)
REVERT: C   95 LYS cc_start: 0.9020 (tptt) cc_final: 0.8673 (tptm)
REVERT: D   33 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7795 (mtp-110)
REVERT: E  125 GLN cc_start: 0.8445 (mt0) cc_final: 0.8000 (mp10)
REVERT: E  129 ARG cc_start: 0.8352 (ttp80) cc_final: 0.7602 (tpt170)
REVERT: F   88 TYR cc_start: 0.8429 (m-10) cc_final: 0.7842 (m-10)
REVERT: H  119 THR cc_start: 0.9481 (t) cc_final: 0.9240 (t)
REVERT: K   66 THR cc_start: 0.8264 (m) cc_final: 0.7973 (m)
REVERT: K   68 ARG cc_start: 0.7439 (ptp90) cc_final: 0.7213 (mtm180)
REVERT: L    8 LYS cc_start: 0.8704 (mppt) cc_final: 0.8322 (tptp)
REVERT: L   69 PHE cc_start: 0.7552 (m-80) cc_final: 0.7240 (m-80)
REVERT: L   74 TYR cc_start: 0.8443 (t80) cc_final: 0.8038 (t80)
REVERT: L   97 LEU cc_start: 0.8373 (tt) cc_final: 0.8108 (tp)
REVERT: L  134 TYR cc_start: 0.6814 (t80) cc_final: 0.6481 (t80)
REVERT: L  145 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.5660 (m-10)
  outliers start: 16
  outliers final: 8
  residues processed: 214
  average time/residue: 0.3355
  time to fit residues: 97.6174
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 195
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
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 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:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 120 optimal weight:    4.9990
   chunk 124 optimal weight:   10.0000
   chunk 85 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 118 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.126325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.076562 restraints weight = 46633.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.076623 restraints weight = 27287.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.077106 restraints weight = 19213.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  15482  Z= 0.242
  Angle     :  0.644  12.127  22186  Z= 0.355
  Chirality :  0.038   0.287   2516
  Planarity :  0.005   0.056   1794
  Dihedral  : 28.860 175.439   4413
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.45 %
    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:  1.77 (0.26), residues: 1057
  helix:  2.18 (0.21), residues: 649
  sheet:  1.19 (0.73), residues: 50
  loop : -0.75 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L  93 
 HIS   0.004   0.001   HIS L   0 
 PHE   0.044   0.002   PHE L  62 
 TYR   0.014   0.002   TYR H  83 
 ARG   0.008   0.001   ARG K  55 

Details of bonding type rmsd
  link_TRANS           : bond        0.00136 (    2)
  link_TRANS           : angle       0.46961 (    6)
  hydrogen bonds       : bond        0.05278 (  843)
  hydrogen bonds       : angle       3.44518 ( 2151)
  metal coordination   : bond        0.02081 (    8)
  metal coordination   : angle       5.87787 (    9)
  covalent geometry    : bond        0.00567 (15472)
  covalent geometry    : angle       0.63269 (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
  217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.9110 (tptt) cc_final: 0.8720 (tptm)
REVERT: D   33 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7656 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8874 (pm20) cc_final: 0.8536 (pm20)
REVERT: E  125 GLN cc_start: 0.8586 (mt0) cc_final: 0.8236 (mt0)
REVERT: H  119 THR cc_start: 0.9571 (t) cc_final: 0.9338 (t)
REVERT: K   68 ARG cc_start: 0.7764 (ptp90) cc_final: 0.7384 (mtm180)
REVERT: L    8 LYS cc_start: 0.8990 (mppt) cc_final: 0.8553 (tptp)
REVERT: L   74 TYR cc_start: 0.8639 (t80) cc_final: 0.8177 (t80)
REVERT: L   75 HIS cc_start: 0.8770 (t-90) cc_final: 0.8414 (t-90)
REVERT: L  134 TYR cc_start: 0.7755 (t80) cc_final: 0.7145 (t80)
REVERT: L  145 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.6067 (m-10)
  outliers start: 22
  outliers final: 17
  residues processed: 207
  average time/residue: 0.3366
  time to fit residues: 94.6957
Evaluate side-chains
  208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 190
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
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   56 GLU
Chi-restraints excluded: chain C residue   62 ILE
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  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
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
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 123 optimal weight:    8.9990
   chunk 52 optimal weight:    0.7980
   chunk 128 optimal weight:    9.9990
   chunk 73 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 118 optimal weight:    1.9990
   chunk 111 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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
M  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.127520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.077568 restraints weight = 49650.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.077707 restraints weight = 28877.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.078505 restraints weight = 20992.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
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   0.047  15482  Z= 0.183
  Angle     :  0.621  13.149  22186  Z= 0.342
  Chirality :  0.036   0.317   2516
  Planarity :  0.004   0.047   1794
  Dihedral  : 28.820 176.253   4413
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.07 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.26), residues: 1057
  helix:  2.23 (0.21), residues: 648
  sheet:  1.16 (0.73), residues: 50
  loop : -0.71 (0.31), residues: 359

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   0.044   0.002   PHE L  62 
 TYR   0.018   0.002   TYR H  83 
 ARG   0.012   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00076 (    2)
  link_TRANS           : angle       0.38745 (    6)
  hydrogen bonds       : bond        0.04742 (  843)
  hydrogen bonds       : angle       3.29071 ( 2151)
  metal coordination   : bond        0.01873 (    8)
  metal coordination   : angle       5.60270 (    9)
  covalent geometry    : bond        0.00415 (15472)
  covalent geometry    : angle       0.61126 (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
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8403 (tp30) cc_final: 0.8103 (mm-30)
REVERT: C   95 LYS cc_start: 0.9050 (tptt) cc_final: 0.8708 (tptm)
REVERT: D   33 ARG cc_start: 0.8271 (mtp-110) cc_final: 0.7733 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8851 (pm20) cc_final: 0.8517 (pm20)
REVERT: E  125 GLN cc_start: 0.8523 (mt0) cc_final: 0.8216 (mt0)
REVERT: H  119 THR cc_start: 0.9550 (t) cc_final: 0.9297 (t)
REVERT: K   68 ARG cc_start: 0.7715 (ptp90) cc_final: 0.7440 (mtm180)
REVERT: L    8 LYS cc_start: 0.8981 (mppt) cc_final: 0.8541 (tptp)
REVERT: L   69 PHE cc_start: 0.7994 (m-80) cc_final: 0.7714 (m-80)
REVERT: L   74 TYR cc_start: 0.8626 (t80) cc_final: 0.8324 (t80)
REVERT: L   75 HIS cc_start: 0.8737 (t-90) cc_final: 0.8469 (t-90)
REVERT: L   93 TRP cc_start: 0.8623 (t-100) cc_final: 0.8366 (t-100)
REVERT: L  134 TYR cc_start: 0.7815 (t80) cc_final: 0.7268 (t80)
REVERT: L  145 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6490 (m-10)
  outliers start: 18
  outliers final: 16
  residues processed: 203
  average time/residue: 0.3381
  time to fit residues: 93.0183
Evaluate side-chains
  208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 191
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
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   62 ILE
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 H residue  122 THR
Chi-restraints excluded: chain K residue   42 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 123 optimal weight:   20.0000
   chunk 42 optimal weight:    0.5980
   chunk 126 optimal weight:    9.9990
   chunk 109 optimal weight:    5.9990
   chunk 115 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.126113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.076193 restraints weight = 48951.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.077150 restraints weight = 26646.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.077601 restraints weight = 18961.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  15482  Z= 0.233
  Angle     :  0.659  13.756  22186  Z= 0.360
  Chirality :  0.038   0.330   2516
  Planarity :  0.004   0.041   1794
  Dihedral  : 28.912 175.341   4413
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.18 %
    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:  1.63 (0.26), residues: 1057
  helix:  2.07 (0.20), residues: 648
  sheet:  1.02 (0.72), residues: 50
  loop : -0.77 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP L  93 
 HIS   0.003   0.001   HIS L  75 
 PHE   0.044   0.002   PHE L  62 
 TYR   0.020   0.002   TYR H  83 
 ARG   0.012   0.001   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00127 (    2)
  link_TRANS           : angle       0.49701 (    6)
  hydrogen bonds       : bond        0.05271 (  843)
  hydrogen bonds       : angle       3.46300 ( 2151)
  metal coordination   : bond        0.02172 (    8)
  metal coordination   : angle       6.50214 (    9)
  covalent geometry    : bond        0.00543 (15472)
  covalent geometry    : angle       0.64583 (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
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.9093 (tptt) cc_final: 0.8714 (tptm)
REVERT: D   33 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7624 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8893 (pm20) cc_final: 0.8590 (pm20)
REVERT: E  125 GLN cc_start: 0.8545 (mt0) cc_final: 0.8283 (mt0)
REVERT: H   59 MET cc_start: 0.8676 (tpp) cc_final: 0.8470 (tpt)
REVERT: H  119 THR cc_start: 0.9548 (t) cc_final: 0.9308 (t)
REVERT: K   68 ARG cc_start: 0.7806 (ptp90) cc_final: 0.7452 (mtm180)
REVERT: L    8 LYS cc_start: 0.9045 (mppt) cc_final: 0.8612 (tptp)
REVERT: L    9 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8426 (mm-30)
REVERT: L   69 PHE cc_start: 0.8204 (m-80) cc_final: 0.7966 (m-80)
REVERT: L   74 TYR cc_start: 0.8681 (t80) cc_final: 0.8275 (t80)
REVERT: L   75 HIS cc_start: 0.8817 (t-90) cc_final: 0.8509 (t-90)
REVERT: L  134 TYR cc_start: 0.8100 (t80) cc_final: 0.7417 (t80)
REVERT: L  145 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6522 (m-10)
  outliers start: 18
  outliers final: 15
  residues processed: 201
  average time/residue: 0.3449
  time to fit residues: 93.9698
Evaluate side-chains
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 190
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
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   62 ILE
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  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 H residue  122 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.127569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.087744 restraints weight = 37403.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.086935 restraints weight = 36869.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.088403 restraints weight = 28329.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.1811

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= 0.168
  Angle     :  0.634  13.837  22186  Z= 0.347
  Chirality :  0.036   0.356   2516
  Planarity :  0.004   0.048   1794
  Dihedral  : 28.832 176.419   4413
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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:  1.84 (0.26), residues: 1057
  helix:  2.24 (0.21), residues: 647
  sheet:  1.22 (0.74), residues: 50
  loop : -0.72 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP L  33 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.045   0.001   PHE L  62 
 TYR   0.018   0.001   TYR H  83 
 ARG   0.014   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00071 (    2)
  link_TRANS           : angle       0.35622 (    6)
  hydrogen bonds       : bond        0.04624 (  843)
  hydrogen bonds       : angle       3.25967 ( 2151)
  metal coordination   : bond        0.01773 (    8)
  metal coordination   : angle       5.28859 (    9)
  covalent geometry    : bond        0.00376 (15472)
  covalent geometry    : angle       0.62502 (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
  208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 192
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.9034 (tptt) cc_final: 0.8689 (tptm)
REVERT: D   33 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7688 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8936 (pm20) cc_final: 0.8619 (pm20)
REVERT: E  125 GLN cc_start: 0.8485 (mt0) cc_final: 0.8139 (mt0)
REVERT: H  119 THR cc_start: 0.9534 (t) cc_final: 0.9301 (t)
REVERT: L   69 PHE cc_start: 0.7591 (m-80) cc_final: 0.7345 (m-80)
REVERT: L   75 HIS cc_start: 0.8407 (t-90) cc_final: 0.8009 (t-90)
REVERT: L  134 TYR cc_start: 0.6722 (t80) cc_final: 0.6279 (t80)
REVERT: L  145 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5941 (m-10)
  outliers start: 16
  outliers final: 14
  residues processed: 202
  average time/residue: 0.3448
  time to fit residues: 94.4108
Evaluate side-chains
  207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 192
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
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   62 ILE
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 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 K residue   42 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 101 optimal weight:    6.9990
   chunk 115 optimal weight:    0.0470
   chunk 33 optimal weight:    0.9990
   chunk 120 optimal weight:    0.5980
   chunk 72 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0030
   chunk 62 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.4688

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.129555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.087915 restraints weight = 36913.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.087200 restraints weight = 29976.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.088134 restraints weight = 26485.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15482  Z= 0.150
  Angle     :  0.642  14.834  22186  Z= 0.347
  Chirality :  0.036   0.348   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 28.751 177.013   4413
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.05 %
    Favored  : 79.55 %
  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:  2.00 (0.26), residues: 1057
  helix:  2.35 (0.21), residues: 648
  sheet:  1.45 (0.75), residues: 49
  loop : -0.64 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L  33 
 HIS   0.006   0.001   HIS L  32 
 PHE   0.035   0.001   PHE L  62 
 TYR   0.018   0.001   TYR H  83 
 ARG   0.014   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00097 (    2)
  link_TRANS           : angle       0.26432 (    6)
  hydrogen bonds       : bond        0.04240 (  843)
  hydrogen bonds       : angle       3.13883 ( 2151)
  metal coordination   : bond        0.01542 (    8)
  metal coordination   : angle       4.67308 (    9)
  covalent geometry    : bond        0.00326 (15472)
  covalent geometry    : angle       0.63519 (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
  208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 195
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8235 (tp30) cc_final: 0.7907 (mm-30)
REVERT: C   95 LYS cc_start: 0.9009 (tptt) cc_final: 0.8657 (tptm)
REVERT: D   33 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7678 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8849 (pm20) cc_final: 0.8520 (pm20)
REVERT: E  125 GLN cc_start: 0.8500 (mt0) cc_final: 0.8138 (mt0)
REVERT: H  119 THR cc_start: 0.9518 (t) cc_final: 0.9285 (t)
REVERT: L    9 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7451 (mm-30)
REVERT: L   69 PHE cc_start: 0.7653 (m-80) cc_final: 0.7392 (m-80)
REVERT: L   74 TYR cc_start: 0.7840 (t80) cc_final: 0.7458 (t80)
REVERT: L   75 HIS cc_start: 0.8369 (t-90) cc_final: 0.7962 (t-90)
  outliers start: 13
  outliers final: 12
  residues processed: 204
  average time/residue: 0.3348
  time to fit residues: 92.6051
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  : 1.096 
-------------------------------------------------------------------------------
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   62 ILE
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 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 50 optimal weight:    0.9990
   chunk 110 optimal weight:    7.9990
   chunk 111 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 108 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.126985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.074689 restraints weight = 57921.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.076699 restraints weight = 30479.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.079072 restraints weight = 21235.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  15482  Z= 0.216
  Angle     :  0.688  14.303  22186  Z= 0.371
  Chirality :  0.038   0.306   2516
  Planarity :  0.004   0.044   1794
  Dihedral  : 28.870 175.915   4413
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.70 %
    Favored  : 78.68 %
  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:  1.80 (0.26), residues: 1057
  helix:  2.18 (0.21), residues: 648
  sheet:  1.44 (0.74), residues: 50
  loop : -0.72 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP L  93 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.052   0.002   PHE L  62 
 TYR   0.030   0.002   TYR L 134 
 ARG   0.013   0.001   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00118 (    2)
  link_TRANS           : angle       0.39993 (    6)
  hydrogen bonds       : bond        0.04987 (  843)
  hydrogen bonds       : angle       3.41853 ( 2151)
  metal coordination   : bond        0.01693 (    8)
  metal coordination   : angle       5.11187 (    9)
  covalent geometry    : bond        0.00501 (15472)
  covalent geometry    : angle       0.68045 (22171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4913.94 seconds
wall clock time: 85 minutes 19.84 seconds (5119.84 seconds total)